scons claims to be a better replacement for make, or rather especially autofoo magic. Unfortunately, it isn't. To me a proper build system should definitely be able to clean up behind itself. The reasoning flying around for why scons isn't able to do so are quite hilarious, ranging from that it doesn't know what it generates (how does it generate them in the first place?) to that it's extensible and thus can't be done properly (then the extensions are broken and should add their clean informations in a hook or such, too). I haven't seen any valid reason for why it shouldn't be able to do so—yet we still seem to need to clean up cruft lying aroud like .scons* files and directories, config.log and of course the build/ directory.
People, if you really want to do some proper build system, don't forget to make it clean up after itself. It shouldn't be the requirement of application developers to fix that (which doesn't really work because a scons target trying to clean the files makes scons crash).